FMO DATABASE

FMODB ID: LJ3N9

Calculation Name: 3R3P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R3P

Chain ID: A

ChEMBL ID:

UniProt ID: A7KV39

Base Structure: X-ray

Registration Date: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-759865.887291
FMO2-HF: Nuclear repulsion	720315.802168
FMO2-HF: Total energy	-39550.085123
FMO2-MP2: Total energy	-39668.206808

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:167:THR)

Summations of interaction energy for fragment #1(A:167:THR)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-8.846	-2.677	4.499	-3.835	-6.834	0.014

Interaction energy analysis for fragmet #1(A:167:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.001

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	169	PRO	0	0.078	0.021	3.651	-1.353	0.455	-0.016	-0.909	-0.883	0.001
4	A	170	GLU	-1	-0.825	-0.896	6.058	0.166	0.166	0.000	0.000	0.000	0.000
5	A	171	ARG	1	0.822	0.905	2.271	-11.046	-8.876	4.112	-2.137	-4.145	0.017
6	A	172	ARG	1	0.942	0.961	2.648	4.812	6.836	0.405	-0.785	-1.644	-0.004
7	A	173	VAL	0	0.013	0.008	4.965	0.254	0.310	-0.001	-0.004	-0.052	0.000
8	A	174	LYS	1	0.801	0.887	8.046	-0.454	-0.454	0.000	0.000	0.000	0.000
9	A	175	GLU	-1	-0.840	-0.909	5.147	0.227	0.338	-0.001	0.000	-0.110	0.000
10	A	176	ILE	0	0.005	0.013	8.829	0.009	0.009	0.000	0.000	0.000	0.000
11	A	177	LEU	0	-0.020	-0.016	11.007	0.066	0.066	0.000	0.000	0.000	0.000
12	A	178	ASP	-1	-0.742	-0.840	11.649	0.397	0.397	0.000	0.000	0.000	0.000
13	A	179	GLU	-1	-0.869	-0.913	12.000	-0.487	-0.487	0.000	0.000	0.000	0.000
14	A	180	MET	0	-0.129	-0.057	14.566	-0.014	-0.014	0.000	0.000	0.000	0.000
15	A	181	ASP	-1	-0.940	-0.957	16.673	0.053	0.053	0.000	0.000	0.000	0.000
16	A	182	ILE	0	-0.056	-0.022	16.800	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	183	VAL	0	0.002	-0.006	16.791	0.028	0.028	0.000	0.000	0.000	0.000
18	A	184	TYR	0	-0.062	-0.068	13.387	0.002	0.002	0.000	0.000	0.000	0.000
19	A	185	PHE	0	-0.075	-0.026	18.098	0.041	0.041	0.000	0.000	0.000	0.000
20	A	186	THR	0	0.029	0.000	12.243	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	187	HIS	0	-0.091	-0.056	10.763	0.086	0.086	0.000	0.000	0.000	0.000
22	A	188	HIS	0	0.014	0.023	16.012	0.029	0.029	0.000	0.000	0.000	0.000
23	A	189	VAL	0	0.010	-0.004	19.637	-0.033	-0.033	0.000	0.000	0.000	0.000
24	A	190	VAL	0	-0.011	-0.014	22.595	0.006	0.006	0.000	0.000	0.000	0.000
25	A	191	GLU	-1	-0.824	-0.887	25.096	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	192	GLY	0	-0.017	-0.005	26.831	-0.007	-0.007	0.000	0.000	0.000	0.000
27	A	193	TRP	0	-0.090	-0.051	23.299	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	194	ASN	0	0.028	0.018	18.363	0.022	0.022	0.000	0.000	0.000	0.000
29	A	195	VAL	0	-0.031	-0.008	18.045	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	196	ALA	0	0.032	0.023	12.558	0.052	0.052	0.000	0.000	0.000	0.000
31	A	197	PHE	0	0.029	0.016	9.817	0.074	0.074	0.000	0.000	0.000	0.000
32	A	198	TYR	0	-0.036	-0.012	15.744	-0.047	-0.047	0.000	0.000	0.000	0.000
33	A	199	LEU	0	0.062	0.020	16.726	0.029	0.029	0.000	0.000	0.000	0.000
34	A	200	GLY	0	0.020	0.026	20.558	0.012	0.012	0.000	0.000	0.000	0.000
35	A	201	LYS	1	0.940	0.950	24.262	0.012	0.012	0.000	0.000	0.000	0.000
36	A	202	LYS	1	0.912	0.969	25.881	0.038	0.038	0.000	0.000	0.000	0.000
37	A	203	LEU	0	0.037	0.033	22.130	-0.018	-0.018	0.000	0.000	0.000	0.000
38	A	204	ALA	0	-0.012	-0.011	19.612	0.021	0.021	0.000	0.000	0.000	0.000
39	A	205	ILE	0	0.022	0.015	13.907	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	206	GLU	-1	-0.837	-0.916	15.361	-0.230	-0.230	0.000	0.000	0.000	0.000
41	A	207	VAL	0	-0.008	-0.004	9.916	-0.051	-0.051	0.000	0.000	0.000	0.000
42	A	208	ASN	0	-0.013	-0.003	12.721	0.058	0.058	0.000	0.000	0.000	0.000
43	A	209	GLY	0	0.131	0.071	12.745	-0.167	-0.167	0.000	0.000	0.000	0.000
44	A	210	VAL	0	-0.008	0.011	14.664	0.109	0.109	0.000	0.000	0.000	0.000
45	A	211	TYR	0	-0.087	-0.055	15.022	0.087	0.087	0.000	0.000	0.000	0.000
46	A	212	TRP	0	0.101	0.048	10.460	-0.136	-0.136	0.000	0.000	0.000	0.000
47	A	213	ALA	0	0.019	0.013	11.534	0.101	0.101	0.000	0.000	0.000	0.000
48	A	214	SER	0	-0.014	-0.009	12.135	0.027	0.027	0.000	0.000	0.000	0.000
49	A	215	LYS	1	0.804	0.920	14.293	0.543	0.543	0.000	0.000	0.000	0.000
50	A	216	GLN	0	-0.001	-0.005	15.762	0.031	0.031	0.000	0.000	0.000	0.000
51	A	217	LYS	1	0.950	0.970	19.462	0.300	0.300	0.000	0.000	0.000	0.000
52	A	218	ASN	0	0.046	0.000	21.421	0.030	0.030	0.000	0.000	0.000	0.000
53	A	219	VAL	0	0.088	0.050	24.159	0.000	0.000	0.000	0.000	0.000	0.000
54	A	220	ASN	0	0.015	0.005	25.576	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	221	LYS	1	0.945	0.982	24.541	0.106	0.106	0.000	0.000	0.000	0.000
56	A	222	ASP	-1	-0.845	-0.920	21.151	-0.266	-0.266	0.000	0.000	0.000	0.000
57	A	223	LYS	1	0.942	0.969	23.874	0.158	0.158	0.000	0.000	0.000	0.000
58	A	224	ARG	1	0.813	0.882	26.673	0.095	0.095	0.000	0.000	0.000	0.000
59	A	225	LYS	1	0.901	0.946	19.453	0.210	0.210	0.000	0.000	0.000	0.000
60	A	226	LEU	0	0.033	0.016	21.649	0.013	0.013	0.000	0.000	0.000	0.000
61	A	227	SER	0	-0.062	-0.027	25.661	0.009	0.009	0.000	0.000	0.000	0.000
62	A	228	GLU	-1	-0.759	-0.863	28.850	-0.077	-0.077	0.000	0.000	0.000	0.000
63	A	229	LEU	0	0.026	0.028	23.510	0.009	0.009	0.000	0.000	0.000	0.000
64	A	230	HIS	0	0.026	0.018	27.649	0.005	0.005	0.000	0.000	0.000	0.000
65	A	231	SER	0	-0.091	-0.058	28.942	0.010	0.010	0.000	0.000	0.000	0.000
66	A	232	LYS	1	0.875	0.928	30.242	0.062	0.062	0.000	0.000	0.000	0.000
67	A	233	GLY	0	-0.032	-0.020	30.824	0.009	0.009	0.000	0.000	0.000	0.000
68	A	234	TYR	0	-0.095	-0.071	24.983	0.002	0.002	0.000	0.000	0.000	0.000
69	A	235	ARG	1	0.872	0.952	24.952	0.115	0.115	0.000	0.000	0.000	0.000
70	A	236	VAL	0	0.009	-0.008	19.884	0.006	0.006	0.000	0.000	0.000	0.000
71	A	237	LEU	0	0.012	0.025	16.774	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	238	THR	0	-0.031	-0.029	16.617	0.005	0.005	0.000	0.000	0.000	0.000
73	A	239	ILE	0	-0.013	-0.003	11.360	0.014	0.014	0.000	0.000	0.000	0.000
74	A	240	GLU	-1	-0.876	-0.948	12.974	-0.683	-0.683	0.000	0.000	0.000	0.000
75	A	241	ASP	-1	-0.895	-0.983	9.474	-1.322	-1.322	0.000	0.000	0.000	0.000
76	A	242	ASP	-1	-0.894	-0.953	9.742	-1.253	-1.253	0.000	0.000	0.000	0.000
77	A	243	GLU	-1	-0.859	-0.912	12.219	-0.706	-0.706	0.000	0.000	0.000	0.000
78	A	244	LEU	0	-0.056	-0.024	6.335	-0.110	-0.110	0.000	0.000	0.000	0.000
79	A	245	ASN	0	-0.116	-0.045	9.223	-0.059	-0.059	0.000	0.000	0.000	0.000
80	A	246	ASP	-1	-0.802	-0.893	10.753	-0.510	-0.510	0.000	0.000	0.000	0.000
81	A	247	ILE	0	0.034	0.004	8.727	0.084	0.084	0.000	0.000	0.000	0.000
82	A	248	ASP	-1	-0.922	-0.949	11.757	-0.370	-0.370	0.000	0.000	0.000	0.000
83	A	249	LYS	1	0.862	0.925	15.259	0.614	0.614	0.000	0.000	0.000	0.000
84	A	250	VAL	0	0.017	0.006	11.053	0.065	0.065	0.000	0.000	0.000	0.000
85	A	251	LYS	1	0.887	0.926	11.800	0.669	0.669	0.000	0.000	0.000	0.000
86	A	252	GLN	0	0.056	0.047	15.034	0.084	0.084	0.000	0.000	0.000	0.000
87	A	253	GLN	0	-0.089	-0.067	16.697	0.077	0.077	0.000	0.000	0.000	0.000
88	A	254	ILE	0	0.042	0.009	12.737	0.049	0.049	0.000	0.000	0.000	0.000
89	A	255	GLN	0	0.008	0.014	17.227	0.047	0.047	0.000	0.000	0.000	0.000
90	A	256	LYS	1	0.877	0.926	19.804	0.351	0.351	0.000	0.000	0.000	0.000
91	A	257	PHE	0	-0.028	0.019	19.231	0.028	0.028	0.000	0.000	0.000	0.000
92	A	258	TRP	0	0.089	0.034	20.024	0.022	0.022	0.000	0.000	0.000	0.000
93	A	259	VAL	0	0.017	-0.004	22.050	0.023	0.023	0.000	0.000	0.000	0.000
94	A	260	THR	0	-0.074	-0.062	24.976	0.016	0.016	0.000	0.000	0.000	0.000
95	A	261	HIS	0	-0.080	-0.039	24.355	0.015	0.015	0.000	0.000	0.000	0.000
96	A	262	ILE	0	-0.049	-0.012	24.330	0.015	0.015	0.000	0.000	0.000	0.000
97	A	263	SER	0	-0.059	-0.012	26.781	0.018	0.018	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:167:THR)